extensions confusion

I have MCEBuddy convert my shows to MP4. Yet the file extension ends up .mpg. Is there any reason the extension isn't .mp4? Do apps check the extension or is that just something for Windows to associate a player?

What profile are you using if you are using the HDHomerun Profile then it will be mpg. If you want to just transcode to mp4 and do not care about keeping the encoded file in the HdHomerun DVR then you must use mp4 profile.